We had a great local-style lunch at Cervejaria O Gordo in Torres Vedras, which is up the coast about 30 minutes from Lisbon.
Recommended in Lisbon:
Cervejaria Ramiro - amazingly fresh seafood and beer: http://www.cervejariaramiro.pt/
Pizzeria Lisboa - We really wanted to go to Cantinho do Avillez, but were too late to get a reservation. I hear great things. We ended up at José Avillez’ pizzeria, which was quite charming and reasonably-priced. They have good salads and pizza, and it was a nice change of pace after eating a lot of protein-based Portuguese food: http://www.joseavillez.pt/en/pizzaria-lisboa
Bom Jardim feels like a tourist trap. It’s one of those places where they put bread and butter on your table and then charge you if you eat it. Their piri piri chicken is fantastic, though and the sauce is really addictive. It’s a nice lunch and they have cute tables in an alley.
A lot of people like 100 Manieras, but I found it to be pretentious, expensive and not mind-blowing. I’d skip it and try to go to one of the Avillez spots.
Hope that helps!